Evaluate gene sets by cell type-specific gene expression

Setup

Load R libraries

library(data.table)
library(ggplot2)
library(ggpubr)
library(tidyr)
library(limma)
library(stringr)

theme_set(theme_classic())

cell_type_name = params$cell_type_name
graph_weight = params$graph_weight

cell_type_name

## [1] "Micro-PVM"

graph_weight

## [1] "5.0"

Check the expression of each gene set in each brain-related cell type

Read in gene info and gene set assignments

file_tag = sprintf("%s_%s", cell_type_name, graph_weight)

assayed_genes = scan(sprintf("output/gene_list_%s.txt", file_tag), 
                     what = character(), sep="\n")

length(assayed_genes)

## [1] 2000

gene_sets = scan(sprintf("output/name_s_%s.txt", file_tag), 
                 what = character(), sep="\n")

gene_sets = sapply(gene_sets, strsplit, split=",")
n_genes   = sapply(gene_sets, length)
names(n_genes) = NULL
summary(n_genes)

##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##   37.00   39.00   40.50   40.45   42.00   43.00

length(n_genes)

## [1] 40

sort(n_genes)

##  [1] 37 38 38 38 38 39 39 39 39 39 39 39 39 40 40 40 40 40 40 40 41 41 41 41 41
## [26] 42 42 42 42 42 42 42 42 42 42 42 42 42 43 43

Find gene symbols using the alias2Symbol function from limma.

a2s = rep(NA, length(assayed_genes))
for(i in 1:length(assayed_genes)){
  gi = assayed_genes[i]
  ai = alias2Symbol(gi)
  if(length(ai) > 1){
    print(gi)
    print(ai)
  }
  a2s[i] = ai[1]
}

table(is.na(a2s))

## 
## FALSE  TRUE 
##  1739   261

table(a2s == assayed_genes, useNA = 'ifany')

## 
## FALSE  TRUE  <NA> 
##    21  1718   261

gene_info = data.table(sym_in_data = assayed_genes, sym_limma = a2s)

gene_info[sym_in_data != sym_limma,]

##     sym_in_data   sym_limma
##  1:       LRRC6     DNAAF11
##  2:    C11orf49      CSTPP1
##  3:   LINC00476 ERCC6L2-AS1
##  4:  HNRNPA1P48   HNRNPA1L3
##  5:  ZRANB2-AS2   ZRANB2-DT
##  6:   LINC00271     AHI1-DT
##  7:    RFX3-AS1     RFX3-DT
##  8:   LINC00884  ATP13A3-DT
##  9:   FBXO30-DT    EPM2A-DT
## 10:   LINC00894    EOLA2-DT
## 11:   COX10-AS1    COX10-DT
## 12:   LINC01184  SLC12A2-DT
## 13: FAM198B-AS1  GASK1B-AS1
## 14:     C5orf17   LINC02899
## 15: C8orf37-AS1 CFAP418-AS1
## 16:   LINC01146       HISLA
## 17:      BTBD11       ABTB3
## 18:       H2BU1      H2BC26
## 19:      SKIV2L       SKIC2
## 20:     FAM155A       NALF1
## 21:  CTB-41I6.2   PIK3R5-DT
##     sym_in_data   sym_limma

gene_info[, gene_symbol := sym_in_data]
gene_info[which(sym_in_data != sym_limma & (gene_symbol != "MT-CO2")), 
                gene_symbol := sym_limma]

dim(gene_info)

## [1] 2000    3

gene_info[1:5,]

##    sym_in_data sym_limma gene_symbol
## 1:        CFTR      CFTR        CFTR
## 2:        ICA1      ICA1        ICA1
## 3:        PDK4      PDK4        PDK4
## 4:       CALCR     CALCR       CALCR
## 5:       ABCB4     ABCB4       ABCB4

t1 = table(gene_info$gene_symbol)
table(t1)

## t1
##    1 
## 2000

Read in cell type-specific expression data

Gene set annotations (by gene symbols) were downloaded from MSigDB website.

ct = fread("../Annotation/rna_single_cell_type.tsv.gz")
dim(ct)

## [1] 1587110       4

ct[1:5,]

##               Gene Gene name             Cell type  nTPM
## 1: ENSG00000000003    TSPAN6            Adipocytes 149.5
## 2: ENSG00000000003    TSPAN6 Alveolar cells type 1   6.1
## 3: ENSG00000000003    TSPAN6 Alveolar cells type 2  10.5
## 4: ENSG00000000003    TSPAN6            Astrocytes  13.9
## 5: ENSG00000000003    TSPAN6               B-cells   1.5

length(unique(ct$`Cell type`))

## [1] 79

table(ct$`Cell type`)

## 
##                      Adipocytes           Alveolar cells type 1 
##                           20090                           20090 
##           Alveolar cells type 2                      Astrocytes 
##                           20090                           20090 
##                         B-cells             Basal keratinocytes 
##                           20090                           20090 
##           Basal prostatic cells         Basal respiratory cells 
##                           20090                           20090 
## Basal squamous epithelial cells                   Bipolar cells 
##                           20090                           20090 
##          Breast glandular cells      Breast myoepithelial cells 
##                           20090                           20090 
##                  Cardiomyocytes                  Cholangiocytes 
##                           20090                           20090 
##                      Club cells           Collecting duct cells 
##                           20090                           20090 
##        Cone photoreceptor cells                Cytotrophoblasts 
##                           20090                           20090 
##                 dendritic cells              Distal enterocytes 
##                           20090                           20090 
##            Distal tubular cells                    Ductal cells 
##                           20090                           20090 
##                Early spermatids      Endometrial ciliated cells 
##                           20090                           20090 
##       Endometrial stromal cells               Endothelial cells 
##                           20090                           20090 
##           Enteroendocrine cells                 Erythroid cells 
##                           20090                           20090 
##              Excitatory neurons        Exocrine glandular cells 
##                           20090                           20090 
##       Extravillous trophoblasts                     Fibroblasts 
##                           20090                           20090 
##   Gastric mucus-secreting cells     Glandular and luminal cells 
##                           20090                           20090 
##                    granulocytes                 Granulosa cells 
##                           20090                           20090 
##                     Hepatocytes                  Hofbauer cells 
##                           20090                           20090 
##                Horizontal cells              Inhibitory neurons 
##                           20090                           20090 
##         Intestinal goblet cells                       Ionocytes 
##                           20090                           20090 
##                   Kupffer cells                Langerhans cells 
##                           20090                           20090 
##                 Late spermatids                    Leydig cells 
##                           20090                           20090 
##                     Macrophages                     Melanocytes 
##                           20090                           20090 
##                Microglial cells                       monocytes 
##                           20090                           20090 
##           Mucus glandular cells               Muller glia cells 
##                           20090                           20090 
##                        NK-cells Oligodendrocyte precursor cells 
##                           20090                           20090 
##                Oligodendrocytes      Pancreatic endocrine cells 
##                           20090                           20090 
##                    Paneth cells               Peritubular cells 
##                           20090                           20090 
##                    Plasma cells       Prostatic glandular cells 
##                           20090                           20090 
##            Proximal enterocytes          Proximal tubular cells 
##                           20090                           20090 
##      Respiratory ciliated cells         Rod photoreceptor cells 
##                           20090                           20090 
##             Salivary duct cells                   Schwann cells 
##                           20090                           20090 
##          Serous glandular cells                   Sertoli cells 
##                           20090                           20090 
##               Skeletal myocytes             Smooth muscle cells 
##                           20090                           20090 
##                   Spermatocytes                   Spermatogonia 
##                           20090                           20090 
##       Squamous epithelial cells        Suprabasal keratinocytes 
##                           20090                           20090 
##            Syncytiotrophoblasts                         T-cells 
##                           20090                           20090 
##                     Theca cells         Thymic epithelial cells 
##                           20090                           20090 
##          Undifferentiated cells 
##                           20090

cell_group = fread("../Annotation/rna_single_cell_type_brain.tsv")
dim(cell_group)

## [1] 16  2

cell_group[1:2,]

##             Cell_type Cell_group
## 1: Excitatory neurons   Neuronal
## 2: Inhibitory neurons   Neuronal

ct = ct[`Cell type` %in% cell_group$Cell_type,]
table(ct$`Cell type`)

## 
##                      Astrocytes                         B-cells 
##                           20090                           20090 
##                   Bipolar cells        Cone photoreceptor cells 
##                           20090                           20090 
##              Excitatory neurons                Horizontal cells 
##                           20090                           20090 
##              Inhibitory neurons                Microglial cells 
##                           20090                           20090 
##               Muller glia cells Oligodendrocyte precursor cells 
##                           20090                           20090 
##                Oligodendrocytes                    Plasma cells 
##                           20090                           20090 
##         Rod photoreceptor cells                   Schwann cells 
##                           20090                           20090 
##                         T-cells 
##                           20090

Check gene expression for each gene set

dim(gene_info)

## [1] 2000    3

for(k in 1:length(gene_sets)){
  if(length(gene_sets[[k]]) < 10) { next }
  
  print(k)
  set_k = paste0("set_", k)
  print(gene_sets[[k]])
  
  genes = gene_info[sym_in_data %in% gene_sets[[k]], gene_symbol]

  n_genes = sum(genes %in% ct$`Gene name`)
  print(sprintf("found %d genes.", n_genes))

  if(n_genes == 0) { next }

  df = ct[`Gene name` %in% genes,]
  dim(df)
  df[1:2,]
  
  stopifnot(all(str_to_lower(df$`Cell type`) %in% 
                  str_to_lower(cell_group$Cell_type)))
  
  mat1 = match(str_to_lower(df$`Cell type`), 
               str_to_lower(cell_group$Cell_type))
  
  df = cbind(df, cell_group[mat1,])
  df[1:2,]
  
  df$Cell_type = factor(df$Cell_type, levels = cell_group$Cell_type)
  df$Cell_group = factor(df$Cell_group, 
                         levels = unique(cell_group$Cell_group))
  
  p1 = ggplot(df, aes(x=Cell_type, y=log10(nTPM + 0.1), fill=Cell_group)) + 
    geom_boxplot() + xlab("Cell type") + ggtitle(set_k) + 
    theme(axis.text.x = element_text(angle = 45, hjust = 1)) + 
    scale_fill_brewer(palette="RdBu")

  print(p1)
}

## [1] 1
##  [1] "PFN2"      "ABCC1"     "STMN2"     "FBN2"      "NFIX"      "VCAN"     
##  [7] "ABCA7"     "FAM107B"   "PLEKHH3"   "ANO8"      "RAP1GAP"   "ITPKC"    
## [13] "NDFIP2"    "DGKH"      "HSF4"      "HAVCR1"    "PFKFB4"    "CYTIP"    
## [19] "HIF3A"     "HIP1"      "KIF1A"     "RAMP1"     "KDM6B"     "MACROD1"  
## [25] "DNAJB2"    "MYO1G"     "GUK1"      "CAMK4"     "FBXO27"    "GMEB1"    
## [31] "ANKZF1"    "OTUD1"     "ZBTB7A"    "TRNAU1AP"  "TNFAIP8L3" "ZBTB7C"   
## [37] "SESTD1"    "CD247"     "SLC12A8"   "LUCAT1"   
## [1] "found 39 genes."

## [1] 2
##  [1] "SP140"         "GAREM1"        "AZIN2"         "LINC00467"    
##  [5] "HESX1"         "UCN"           "PLD4"          "DENND2B"      
##  [9] "SPTLC3"        "CYSLTR1"       "MCMDC2"        "CATSPERE"     
## [13] "CAPS2"         "CLEC9A"        "LINC01285"     "AC003090.1"   
## [17] "LINC01357"     "TMEM72-AS1"    "FTCDNL1"       "RP11-162D16.2"
## [21] "RFX3-AS1"      "LINC02642"     "RPL34-DT"      "RP11-195C7.1" 
## [25] "COX10-AS1"     "RNF217-AS1"    "GMDS-DT"       "RP11-745L13.2"
## [29] "CTC-575N7.1"   "MIR3142HG"     "RP11-630C16.2" "RP11-554D14.6"
## [33] "RP11-72M17.1"  "RP11-187O7.3"  "RP11-323I15.5" "MIR222HG"     
## [37] "RP11-323P17.2" "EIF1B-AS1"     "RP11-281A20.2" "RP11-323F24.5"
## [41] "RP11-111G13.1" "RP11-120L14.1"
## [1] "found 14 genes."

## [1] 3
##  [1] "SYNDIG1"        "CPED1"          "ARL5C"          "SESN3"         
##  [5] "ENPP3"          "C4orf19"        "DEPTOR"         "GHRL"          
##  [9] "ADAMTS15"       "MIR31HG"        "MICOS10"        "MARCHF3"       
## [13] "KBTBD12"        "MAMDC2-AS1"     "LINC00539"      "HCG22"         
## [17] "AC002539.1"     "RP5-1198O20.4"  "RP11-634B7.4"   "LINC01141"     
## [21] "AC073115.6"     "KCNMB2-AS1"     "LINC02008"      "RP11-246A10.1" 
## [25] "XACT"           "LINC02057"      "LINC01258"      "AC008697.1"    
## [29] "LINC02232"      "MAILR"          "RP11-946L16.1"  "LINC02444"     
## [33] "RP11-588H23.3"  "RP11-399K21.11" "LINC02712"      "CCDC28A-AS1"   
## [37] "LINC00506"      "RP11-437L7.2"   "RP11-168F24.3"  "RP11-685G11.1" 
## [41] "RP1-236J16.3"   "RP11-4F5.3"    
## [1] "found 12 genes."

## [1] 4
##  [1] "DUOX1"         "C11orf65"      "ADGRG2"        "ENO4"         
##  [5] "FSIP2"         "AC002463.3"    "ELMO1-AS1"     "TMLHE-AS1"    
##  [9] "SLC8A1-AS1"    "AC105461.1"    "AC096558.1"    "WEE2-AS1"     
## [13] "AC092431.3"    "FSIP2-AS1"     "RNASEH2B-AS1"  "RP11-353M9.1" 
## [17] "RP11-528G1.2"  "RP11-666F17.1" "RP11-123B3.2"  "MYCBP2-AS1"   
## [21] "DIAPH2-AS1"    "CCDC200"       "AC018890.6"    "MEF2C-AS2"    
## [25] "RP11-360F5.1"  "CTD-2227I18.1" "RP11-268P4.5"  "RP11-238K6.1" 
## [29] "RP11-649G15.2" "RP11-463D19.1" "RP11-196H14.2" "RP11-513G19.1"
## [33] "RP11-493L12.3" "RP11-136F16.1" "LMO7-AS1"      "RP11-621L6.2" 
## [37] "RP11-793A3.2"  "CTD-2282P23.2" "RP11-305E17.8" "DISC2"        
## [41] "RP11-1146N6.3" "RP11-314E10.1" "RP3-467L1.4"  
## [1] "found 6 genes."

## [1] 5
##  [1] "TRIM2"         "PTPRB"         "MEIS1"         "BTD"          
##  [5] "FIGN"          "ZNF804B"       "RP11-640F22.1" "CNTN1"        
##  [9] "ADGRL1"        "CELF4"         "CDH20"         "FLT1"         
## [13] "ITGB8"         "DNAH6"         "MICAL2"        "ZNF365"       
## [17] "ADGRL3"        "SPOCK1"        "SCN3A"         "CACNA2D1"     
## [21] "PTPRN2"        "SYN2"          "FGF17"         "SPTBN4"       
## [25] "PDZRN4"        "ZFPM2"         "FUT9"          "CDH4"         
## [29] "GPC5"          "TSHZ2"         "PBX1"          "SYN3"         
## [33] "MIB2"          "TOX"           "RORB"          "SOGA3"        
## [37] "RP11-384F7.2"  "MTRNR2L1"     
## [1] "found 36 genes."

## [1] 6
##  [1] "CELSR3"        "SYT7"          "CSMD2"         "PCSK2"        
##  [5] "ATP8A2"        "RBMS3"         "TENM2"         "CNTN5"        
##  [9] "ZNF385D"       "AK5"           "NCAM2"         "CFAP251"      
## [13] "CLSTN2"        "NRG2"          "CAMK2N1"       "ANKRD30BL"    
## [17] "GABRB1"        "PRICKLE2"      "CSMD3"         "LRFN5"        
## [21] "GREM1"         "SEMA3E"        "HPSE2"         "LRRC3B"       
## [25] "KCTD16"        "FLRT2"         "PTPRT"         "CR1L"         
## [29] "ZNF521"        "LINC00970"     "LINC00632"     "FAM155A"      
## [33] "MIAT"          "AC013463.2"    "SHISA9"        "AC002066.1"   
## [37] "RP11-79E3.2"   "CTC-535M15.2"  "RP11-20D14.3"  "IQCJ-SCHIP1"  
## [41] "RP4-799O8.1"   "RP5-1015P16.1" "RP11-398J12.1"
## [1] "found 31 genes."

## [1] 7
##  [1] "ZFP64"                   "PLAGL1"                 
##  [3] "SPATA6"                  "PEBP4"                  
##  [5] "ARMH4"                   "MTHFD2L"                
##  [7] "NMNAT3"                  "ARHGAP42"               
##  [9] "ATF7IP2"                 "TMC7"                   
## [11] "ACYP2"                   "ZDHHC14"                
## [13] "C5orf64"                 "SPATA13_ENSG00000182957"
## [15] "KCNQ3"                   "SCFD2"                  
## [17] "PRKN"                    "MBD5"                   
## [19] "MIR99AHG"                "HMGA1P4"                
## [21] "MEF2C-AS1"               "CTB-161M19.4"           
## [23] "MRPS30-DT"               "ARHGAP6"                
## [25] "KCNQ2"                   "PILRA"                  
## [27] "BICRAL"                  "SLC26A7"                
## [29] "NPAS3"                   "FUT10"                  
## [31] "ZHX2"                    "KCNQ5"                  
## [33] "GLDN"                    "NPIPB15"                
## [35] "ZNF846"                  "ZDBF2"                  
## [37] "LNCAROD"                 "MYO16-AS1"              
## [39] "LINC02646"               "HCG17"                  
## [41] "RP11-114N19.3"           "RP11-358F13.1"          
## [1] "found 29 genes."

## [1] 8
##  [1] "TMSB10"  "TPD52"   "OXCT1"   "SUSD1"   "MAP2K6"  "ALDOC"   "CCDC18" 
##  [8] "MTHFS"   "TBC1D32" "FOXO1"   "CLIC2"   "IER2"    "C1QA"    "ABAT"   
## [15] "RPL39"   "TWIST2"  "FGR"     "HGF"     "CDK14"   "CDK17"   "DDX3Y"  
## [22] "PGM1"    "NAMPT"   "TPI1"    "SOD2"    "USP9Y"   "PAPOLG"  "HSPH1"  
## [29] "DOCK6"   "ZNF331"  "GNA12"   "NEK7"    "ETS2"    "PTMS"    "PCNT"   
## [36] "AXL"     "CLIC4"   "GLRX"    "FAM210A"
## [1] "found 39 genes."

## [1] 9
##  [1] "SNCAIP"  "LRRC74A" "IL1A"    "IL1B"    "STON2"   "MLIP"    "MACROD2"
##  [8] "ZNF707"  "KCNIP1"  "SKA2"    "HECW1"   "MATK"    "PKD1"    "CTNNA2" 
## [15] "TRHDE"   "RBFOX1"  "PHLPP1"  "EPHA4"   "KDM5B"   "EMILIN2" "FGF2"   
## [22] "KCNH1"   "SNTG1"   "FMN2"    "LRP1B"   "DLGAP1"  "KCND3"   "DPP10"  
## [29] "PCDH9"   "EFNA5"   "KCND2"   "NELL2"   "RALYL"   "KCNIP4"  "MAGI2"  
## [36] "GRM7"    "MICAL3" 
## [1] "found 37 genes."

## [1] 10
##  [1] "ADAM28"    "ST6GAL1"   "APBB1IP"   "TMEM156"   "PLAC8"     "KCNMB1"   
##  [7] "RASGEF1C"  "KCNMA1"    "TSPAN7"    "AUTS2"     "PRMT9"     "NXN"      
## [13] "ZNF608"    "GPR34"     "TLN2"      "DLEU1"     "SLC8A1"    "SRGAP3"   
## [19] "KIF9-AS1"  "LINC01091" "MIR100HG"  "PRANCR"    "MRC1"      "RNASET2"  
## [25] "DOCK3"     "PCSK5"     "TMED8"     "TIMP1"     "RGCC"      "LIFR"     
## [31] "NR4A3"     "TMEM115"   "SLC2A5"    "SPRY1"     "RBFOX3"    "DHRS13"   
## [37] "ROBO1"     "AIDA"      "TSPAN4"    "SNHG14"   
## [1] "found 34 genes."

## [1] 11
##  [1] "OPHN1"         "LRRC6"         "RAB40B"        "CFAP74"       
##  [5] "BEND6"         "ADGRG5"        "PLXDC1"        "RNF180"       
##  [9] "CCDC171"       "MT1E"          "LINC00476"     "PLCXD3"       
## [13] "COL25A1"       "AC007879.5"    "ENTPD3-AS1"    "TSBP1-AS1"    
## [17] "RP11-445F6.2"  "TEX41"         "LMCD1-AS1"     "RP13-188A5.1" 
## [21] "LINC00271"     "LINC02884"     "RORA-AS1"      "BDNF-AS"      
## [25] "LINC02211"     "MIR4300HG"     "STX18-AS1"     "RP11-130F10.1"
## [29] "RP11-692D12.1" "RP11-679C8.2"  "LINC02055"     "SMIM35"       
## [33] "RP11-493L12.4" "LINC00639"     "CTD-2336H13.2" "LINC01374"    
## [37] "RP11-495L19.1" "RP11-622O11.6" "RP6-91H8.6"    "RP4-545L17.11"
## [41] "RP11-321P16.3" "HTR1E"        
## [1] "found 13 genes."

## [1] 12
##  [1] "SNX24"         "ARHGEF18"      "PDE4D"         "XKR6"         
##  [5] "RP11-131L23.1" "SLC16A1-AS1"   "JARID2"        "MSR1"         
##  [9] "ARAP2"         "PDE4A"         "FAM50A"        "CPSF1"        
## [13] "PRKAG2"        "TSHZ3"         "SEM1"          "FNBP1L"       
## [17] "CAMKMT"        "RSU1"          "SLC2A13"       "ACSL1"        
## [21] "RPP38"         "RASA2"         "ST3GAL2"       "ACOT11"       
## [25] "MTSS1"         "KLHL6"         "SH3PXD2B"      "PACS1"        
## [29] "PDE4B"         "OSBP2"         "PARVB"         "CTD-3088G3.8" 
## [33] "COL27A1"       "LINC00862"     "AS3MT"         "RP11-37N22.1" 
## [37] "FAM229A"       "AC067959.1"    "RP11-13N12.1"  "RP11-344F5.1" 
## [41] "RP11-249L21.6"
## [1] "found 32 genes."

## [1] 13
##  [1] "EPB41L2"  "EPB41L3"  "TDRD3"    "CALD1"    "SMAD6"    "STAMBPL1"
##  [7] "ALDH7A1"  "ZNRF1"    "NSMAF"    "AMPH"     "IRAK3"    "ARHGEF10"
## [13] "DOT1L"    "PPARD"    "RLF"      "AKT3"     "CTSD"     "ELL2"    
## [19] "RUNX2"    "ARHGAP22" "IRAK2"    "PHF21A"   "GLUL"     "FAM117B" 
## [25] "PELI2"    "USP53"    "ARID5B"   "RIT2"     "PDE3B"    "AGPAT5"  
## [31] "EPB41"    "RUNX1"    "G6PD"     "PPIP5K1"  "TMEM51"   "AFF1"    
## [37] "PELI1"    "RGL3"    
## [1] "found 38 genes."

## [1] 14
##  [1] "PRDM11"   "CD74"     "P3H2"     "NLRP1"    "DAAM1"    "ITPR2"   
##  [7] "ABCC4"    "DOCK10"   "LPAR6"    "BCAS3"    "MED12L"   "CCDC102B"
## [13] "COPG2"    "KIF26B"   "ARHGAP25" "P2RY12"   "NAALADL2" "CACNB4"  
## [19] "DYNC2H1"  "SLC1A3"   "RFX3"     "RFX2"     "DOCK9"    "LAPTM4B" 
## [25] "RAPGEF1"  "PTPRE"    "SSH2"     "SDK1"     "FER"      "MGAT5"   
## [31] "FMNL2"    "OXR1"     "KIF5C"    "BNC2"     "KLC2"     "LONRF3"  
## [37] "OPCML"    "GDI1"     "NEAT1"   
## [1] "found 38 genes."

## [1] 15
##  [1] "ETV1"     "PRKCQ"    "MGLL"     "RPH3A"    "PITPNM2"  "RNF157"  
##  [7] "TAGAP"    "ATF5"     "GTF2IRD1" "ADAM22"   "KCNAB2"   "RAB27A"  
## [13] "TNS1"     "ZNF586"   "PTPN4"    "ARRDC2"   "ADAP1"    "NPDC1"   
## [19] "DCUN1D4"  "SASH1"    "CCND3"    "HPCAL1"   "IQSEC2"   "ZC4H2"   
## [25] "GYPC"     "RASGRP3"  "MSI2"     "MALT1"    "C11orf80" "GOLIM4"  
## [31] "LPL"      "ALOX15B"  "ZDHHC20"  "CADM1"    "IFNLR1"   "ARL4C"   
## [37] "CARD11"   "UNC13B"  
## [1] "found 38 genes."

## [1] 16
##  [1] "MCF2L2"        "ANGPT2"        "PROCR"         "CST3"         
##  [5] "IL7"           "NEK11"         "MMP24"         "SGCE"         
##  [9] "IER3"          "PDE5A"         "C1QC"          "BTG2"         
## [13] "PAQR3"         "FILIP1L"       "SLC35G2"       "GRIK1"        
## [17] "MIR4435-2HG"   "OLR1"          "H2BC4"         "ENTPD1-AS1"   
## [21] "RPL41"         "RP4-568F9.6"   "DENND6A-AS1"   "RP11-452H21.1"
## [25] "RNF213-AS1"    "ABHD15-AS1"    "KCNQ1OT1"      "MMP28"        
## [29] "H2AC19"        "LINC00624"     "GS1-98E2.1"    "TGFB2"        
## [33] "RNMT"          "COL5A1"        "ALCAM"         "PPM1E"        
## [37] "H1-0"          "CEBPD"         "RP11-384C4.7" 
## [1] "found 28 genes."

## [1] 17
##  [1] "DERA"          "TYMP"          "MAP3K8"        "SLC2A9"       
##  [5] "FLVCR2"        "TBC1D14"       "EPSTI1"        "BCL2A1"       
##  [9] "PTH2R"         "PSTPIP2"       "DISP1"         "LY96"         
## [13] "FAM227B"       "PNMA3"         "CHSY3"         "RP11-154H12.3"
## [17] "SAMD4A"        "LIMCH1"        "GRK3"          "MAN1A1"       
## [21] "FRMD4B"        "PADI2"         "CDH26"         "CHSY1"        
## [25] "TLR2"          "TIAM2"         "SLC25A37"      "CFDP1"        
## [29] "CDCP1"         "TNFRSF11B"     "LRFN4"         "SSTR2"        
## [33] "TLR5"          "CYRIA"         "GK"            "GCC2-AS1"     
## [37] "STARD10"       "ZNF407"        "MIR181A1HG"    "FMN1"         
## [41] "RP11-368L12.1"
## [1] "found 37 genes."

## [1] 18
##  [1] "CASS4"         "MPP2"          "RP11-160E2.6"  "LRRC7"        
##  [5] "ARHGAP10"      "SLC26A3"       "PCDH11Y"       "CPE"          
##  [9] "MOB3B"         "PDZD2"         "SEMA6D"        "CDH18"        
## [13] "CLVS2"         "CNKSR2"        "CRIM1"         "SORCS3"       
## [17] "EDIL3"         "ADGRV1"        "NLGN1"         "CTNND2"       
## [21] "ADCY5"         "CNTNAP2"       "RESF1"         "CADM2"        
## [25] "RIMS2"         "NRXN1"         "CSMD1"         "ANKS1B"       
## [29] "PRKG1"         "NRG3"          "SLIT1"         "POTEG"        
## [33] "KAZN"          "MEG3"          "BASP1-AS1"     "ROR1-AS1"     
## [37] "LINC01320"     "USP2-AS1"      "CPEB2-DT"      "LINC00558"    
## [41] "RP11-81K2.1"   "RP11-396B14.2"
## [1] "found 32 genes."

## [1] 19
##  [1] "OSBPL6"  "RALGPS2" "SLC10A7" "F13A1"   "GAS2L3"  "MAGI1"   "PTPN14" 
##  [8] "BACH1"   "TIAM1"   "FBXL13"  "PLEKHA7" "SH3RF3"  "NCKAP5"  "PLEKHA5"
## [15] "RORA"    "FNDC3B"  "SMARCD3" "TBL1X"   "TRPS1"   "POU6F2"  "MEGF9"  
## [22] "DENND1A" "STARD13" "DENND4C" "CPNE8"   "RGL1"    "THRB"    "FARP1"  
## [29] "ASAP1"   "LONRF1"  "SRSF12"  "AGAP1"   "LDLRAD4" "FAM110B" "TANC2"  
## [36] "PEAK1"   "CHST15"  "LIMK2"   "SIPA1L1"
## [1] "found 39 genes."

## [1] 20
##  [1] "ICA1"          "PER3"          "GPATCH2"       "GDAP1"        
##  [5] "WLS"           "CCDC170"       "ZRANB3"        "CHN1"         
##  [9] "AHI1"          "EFCAB11"       "SPAG16"        "TRPC1"        
## [13] "IRAK1BP1"      "MMS22L"        "NRGN"          "CACNA1D"      
## [17] "SYCE2"         "MAMDC2"        "RIC3"          "DTWD2"        
## [21] "DENND5B"       "LCLAT1"        "SCAI"          "HRH1"         
## [25] "KCNMB2"        "CARNMT1-AS1"   "RANBP17"       "ZNF10"        
## [29] "RP11-413N10.3" "ATP9A"         "GABRG2"        "CACNA1B"      
## [33] "CACNA1C"       "FAT3"          "PCDH7"         "FRMD3"        
## [37] "MSRA"          "UNC5C"         "RYR2"         
## [1] "found 37 genes."

## [1] 21
##  [1] "DHRS9"      "EPDR1"      "MID1"       "APBA1"      "GCNT2"     
##  [6] "AKAP7"      "NRN1"       "DTD1"       "METTL25"    "MIS18BP1"  
## [11] "LANCL2"     "LYVE1"      "SLC22A23"   "IRF8"       "AIG1"      
## [16] "CD226"      "TMEM169"    "EMB"        "S100Z"      "GAP43"     
## [21] "MBOAT1"     "PROS1"      "KIAA0825"   "DNAH14"     "CCDC7"     
## [26] "C12orf75"   "RASSF2"     "IL27RA"     "E2F3"       "SLC16A10"  
## [31] "KLHL24"     "HELLS"      "AFDN"       "ZBTB46"     "SLC41A2"   
## [36] "SLC12A6"    "PPP1R9A"    "SERTAD2"    "AC025171.1"
## [1] "found 38 genes."

## [1] 22
##  [1] "RIPOR2"         "MCTP2"          "GLT1D1"         "TMEM151B"      
##  [5] "KIF5C-AS1"      "MTRNR2L8"       "TRG-AS1"        "MAMLD1"        
##  [9] "GALNT16"        "KATNAL1"        "AK1"            "SNX25"         
## [13] "ADAM23"         "ATP8A1"         "PATJ"           "PGGHG"         
## [17] "PAM"            "BTBD11"         "PITPNC1"        "FBXO32"        
## [21] "ZFYVE28"        "ARHGEF3"        "RANBP3L"        "AMER2"         
## [25] "KLF13"          "CXXC5"          "TBC1D10C"       "XKR9"          
## [29] "AC093843.1"     "SATB1-AS1"      "RP11-47I22.3"   "CYP1B1-AS1"    
## [33] "SLC5A4-AS1"     "RMST"           "RP11-429A20.3"  "FMNL1-DT"      
## [37] "MTRNR2L12"      "LINC00551"      "CH507-528H12.1" "RP11-596C23.6" 
## [41] "RENO1"          "RP11-335E8.3"  
## [1] "found 26 genes."

## [1] 23
##  [1] "MUSK"          "EFR3B"         "CECR2"         "LIPG"         
##  [5] "NME3"          "PLAT"          "OGN"           "ECM2"         
##  [9] "PLGRKT"        "PODXL2"        "SLC5A9"        "GALNT12"      
## [13] "PLAU"          "FMO5"          "ITM2C"         "AIM2"         
## [17] "GPR85"         "TMEM52B"       "BEAN1"         "GLYATL1"      
## [21] "ARSJ"          "LTC4S"         "RP11-281P23.2" "RP11-517O13.1"
## [25] "TSIX"          "FSTL4"         "SERPINE1"      "GALNT18"      
## [29] "SLC6A8"        "LYPD5"         "ARSK"          "GPRC5C"       
## [33] "MAMDC4"        "DGAT1"         "SH3BGRL2"      "TBKBP1"       
## [37] "AF064858.6"    "ARHGEF25"      "AGBL1"        
## [1] "found 35 genes."

## [1] 24
##  [1] "SIGLEC1"       "BEX1"          "ADGRA3"        "PAPSS2"       
##  [5] "PVT1"          "LINC00923"     "DISC1FP1"      "ST3GAL1"      
##  [9] "TENM1"         "STAB1"         "HIVEP2"        "HDHD5"        
## [13] "MAP3K20"       "LILRB5"        "MXI1"          "GTDC1"        
## [17] "HS3ST2"        "CEMIP2"        "GPNMB"         "NIBAN2"       
## [21] "RASGEF1B"      "ST18"          "JAML"          "PLPP3"        
## [25] "ATOH8"         "MCTP1"         "TMTC2"         "TPRG1"        
## [29] "DPYD"          "IARS1"         "ERO1A"         "DIRC3"        
## [33] "TRHDE-AS1"     "RP11-657O9.1"  "RP11-696N14.1" "SELENOP"      
## [37] "LINC02698"     "CLEC5A"        "LINC01138"     "CH507-513H4.1"
## [41] "RP11-475M20.2"
## [1] "found 30 genes."

## [1] 25
##  [1] "SLC26A4"                 "PRTFDC1"                
##  [3] "PEX7"                    "ZSCAN5A"                
##  [5] "CDYL2"                   "SLC9A7"                 
##  [7] "MYO9A"                   "ZFY"                    
##  [9] "WNT2B"                   "DRAM1"                  
## [11] "PXDNL"                   "LRRC4C"                 
## [13] "CLEC1A"                  "ME3"                    
## [15] "AMN1"                    "NEK10"                  
## [17] "GPHN"                    "SLC35E3"                
## [19] "SLC48A1"                 "FADS3"                  
## [21] "AC023469.1"              "ARL17B"                 
## [23] "SGO1-AS1"                "LINC01762"              
## [25] "RP11-147G16.1"           "RP11-154D17.1"          
## [27] "RP11-305L7.3"            "IFITM10"                
## [29] "RP11-17A1.3"             "SBF2-AS1"               
## [31] "RP1-179N16.6"            "LINC01609"              
## [33] "RP11-351A11.1"           "RP11-707P17.1"          
## [35] "CTB-41I6.2"              "RMRP_ENSG00000269900"   
## [37] "SCARNA2_ENSG00000270066" "LL22NC03-2H8.5"         
## [39] "AC003099.2"              "C2orf27A"               
## [1] "found 22 genes."

## [1] 26
##  [1] "PLPP1"         "ADGRD1"        "PLEK"          "CYREN"        
##  [5] "CENPK"         "PCBD2"         "ERMN"          "ARHGAP20"     
##  [9] "SLC49A4"       "HERC6"         "UBE2Q2"        "WDPCP"        
## [13] "ABCA5"         "TMEM144"       "NLGN4Y"        "FGGY"         
## [17] "B3GNT5"        "TTTY14"        "PCED1B"        "MS4A4E"       
## [21] "LINC02649"     "RP11-202G18.1" "ZRANB2-AS2"    "RP11-557H15.4"
## [25] "RP11-142A5.1"  "LINC00894"     "LINC01376"     "ARHGAP8"      
## [29] "GPRC5D-AS1"    "RP11-381K20.2" "LINC01572"     "H2BC7"        
## [33] "RP11-419I17.1" "RP1-111C20.3"  "RP11-19D22.1"  "RP11-574F11.4"
## [37] "RP11-221G19.1" "SESN1"         "STN1"          "TMEM65"       
## [41] "MFSD4B"        "ZC3H6"        
## [1] "found 26 genes."

## [1] 27
##  [1] "CARMIL1"       "SSPN"          "PIGC"          "AGBL3"        
##  [5] "FOLR2"         "CYTL1"         "GLIPR1L1"      "FLJ40194"     
##  [9] "DLEU7"         "EYS"           "FAM177B"       "HNRNPA1P48"   
## [13] "EDNRB-AS1"     "LINC01375"     "RP11-526K17.2" "RP11-142M10.2"
## [17] "SRGAP2-AS1"    "COA6-AS1"      "ARHGAP15-AS1"  "IPO9-AS1"     
## [21] "AC007682.1"    "RAP2C-AS1"     "UFL1-AS1"      "ITGA9-AS1"    
## [25] "FBXO30-DT"     "LINC00996"     "RP11-712B9.2"  "RP11-796E2.4" 
## [29] "LINC02742"     "CTD-2537O9.1"  "RP11-370I10.2" "RHOXF1-AS1"   
## [33] "RP11-516C1.1"  "ZNF528-AS1"    "MIR223HG"      "RP11-74J13.8" 
## [37] "RP1-80B9.4"    "RP11-237N2.1"  "RP11-264E23.4" "RP11-7F3.1"   
## [41] "AC009166.9"    "RP11-56I23.2" 
## [1] "found 10 genes."

## [1] 28
##  [1] "LILRB2"        "HTR2B"         "OVCH1-AS1"     "GRAMD4"       
##  [5] "PPP1R15A"      "GADD45B"       "RNF24"         "GYS1"         
##  [9] "IL4I1"         "APBB3"         "GBE1"          "TREM1"        
## [13] "CHI3L1"        "GDF11"         "PLXNC1"        "RGS16"        
## [17] "MYO10"         "PLIN2"         "HTR7"          "TAMALIN"      
## [21] "IER5"          "NFIL3"         "DDIT4"         "PPP1R3B"      
## [25] "BNIP3"         "RBM44"         "ADGRB1"        "VMO1"         
## [29] "ZNF395"        "NHEJ1"         "EFCAB2"        "LILRB3"       
## [33] "LIMD1-AS1"     "ZSCAN31"       "AF064858.8"    "RP11-661A12.5"
## [37] "HIF1A-AS3"     "MYOCOS"        "CTD-2285E13.1"
## [1] "found 33 genes."

## [1] 29
##  [1] "SCMH1"      "IPCEF1"     "POLA1"      "ARSB"       "RCAN3"     
##  [6] "C3"         "FOXP2"      "RFC3"       "GSTCD"      "FRMD6"     
## [11] "FRMD4A"     "ANO10"      "SFMBT1"     "SOCS6"      "LRRC8C"    
## [16] "ATAD5"      "CA8"        "SLC9A9"     "ZFP36L1"    "SFMBT2"    
## [21] "XIST"       "SCIN"       "CLEC16A"    "WWC3"       "ARHGAP15"  
## [26] "CLNK"       "FOXP1"      "HPCAL4"     "RASSF8"     "ELK1"      
## [31] "FAM13A"     "CSGALNACT1" "MERTK"      "JAZF1"      "ADK"       
## [36] "CRADD"      "RNF150"     "SAMD12"     "MAML2"      "PLCG2"     
## [1] "found 39 genes."

## [1] 30
##  [1] "ZNF532"        "MBNL3"         "PIGL"          "CD69"         
##  [5] "MTERF1"        "TMEM241"       "RALGPS1"       "ADAMTS17"     
##  [9] "TMEM44"        "AOPEP"         "RAB28"         "SMIM14"       
## [13] "SLC9B1"        "PGBD5"         "CDIN1"         "B3GLCT"       
## [17] "PRDX6-AS1"     "TMSB4X"        "LIPE-AS1"      "ALOX12-AS1"   
## [21] "ZNF433-AS1"    "RP11-535M15.1" "CTA-292E10.6"  "LINC01278"    
## [25] "LINC01184"     "RP11-319G6.1"  "RP11-37B2.1"   "LIX1-AS1"     
## [29] "LINC02328"     "CEROX1"        "LINC02666"     "CH17-55D9.1"  
## [33] "RP4-681L3.3"   "OGFRL1"        "ADCY3"         "CCDC107"      
## [37] "ABCG1"         "MARCHF8"       "KCNE1"         "LINC00910"    
## [41] "PIK3IP1-DT"   
## [1] "found 23 genes."

## [1] 31
##  [1] "NEXMIF"                  "TRPM3"                  
##  [3] "NIPAL2"                  "PDE10A"                 
##  [5] "GNLY"                    "UNC80"                  
##  [7] "IGSF11"                  "ADAMTS19"               
##  [9] "BANK1"                   "ADAMTS3"                
## [11] "RFLNA"                   "RTN4RL1"                
## [13] "COL5A2"                  "DOK6"                   
## [15] "LINC01277"               "AC011288.2"             
## [17] "RP3-525N10.2"            "ALG1L9P_ENSG00000248671"
## [19] "RP11-673E1.1"            "FAM66D"                 
## [21] "RP4-809F18.1"            "PSMD7-DT"               
## [23] "COPG2IT1"                "LINC02885"              
## [25] "RP11-320L2.1"            "NALCN"                  
## [27] "FGF14"                   "KCNT1"                  
## [29] "CHD5"                    "OLFM1"                  
## [31] "CBLN2"                   "STXBP5L"                
## [33] "PALM2AKAP2"              "NEGR1"                  
## [35] "LSAMP"                   "CACNA1E"                
## [37] "RP11-191L9.4"            "CTC-340A15.2"           
## [39] "RP11-259O2.1"            "LINC01414"              
## [41] "U91319.1"                "RP11-436D23.1"          
## [1] "found 25 genes."

## [1] 32
##  [1] "IFT43"         "CGNL1"         "EPHB2"         "C11orf49"     
##  [5] "GASK1B"        "RAB39A"        "RNLS"          "ERC2"         
##  [9] "CENPP"         "ATP6AP1L"      "FIRRE"         "LINC01356"    
## [13] "AC097721.2"    "LINC01684"     "C5orf17"       "ATP6V0D1-DT"  
## [17] "RP11-692P14.1" "LCP2"          "ZFAT"          "PAG1"         
## [21] "PRAM1"         "KIAA0513"      "PPFIA2"        "CCDC40"       
## [25] "NR6A1"         "DIXDC1"        "SH3RF1"        "CFAP161"      
## [29] "ZNF143"        "LPCAT4"        "CCDC73"        "SYCP2"        
## [33] "LINC02397"     "C17orf67"      "RP5-864K19.4"  "KLF3-AS1"     
## [37] "AC092835.2"    "RP11-111A21.1" "RP11-154H23.4" "RP11-404C6.6" 
## [1] "found 24 genes."

## [1] 33
##  [1] "CALCR"                     "ACER3"                    
##  [3] "CEACAM1"                   "HAMP"                     
##  [5] "ADGRG6"                    "PARD3B"                   
##  [7] "LDAH"                      "RAB38"                    
##  [9] "PUDP"                      "NPL"                      
## [11] "CH25H"                     "NKD1"                     
## [13] "SAMSN1"                    "MAP3K7CL"                 
## [15] "TNFRSF13C"                 "PUS10"                    
## [17] "DNAJC24"                   "WDR25"                    
## [19] "SDHAF3"                    "LIN52"                    
## [21] "LINC00630"                 "LINC01515"                
## [23] "CCDC26"                    "CDKN2B-AS1"               
## [25] "LINC02432"                 "LINC01094"                
## [27] "LINC01605_ENSG00000253161" "C8orf37-AS1"              
## [29] "RP11-486A14.2"             "LINC01146"                
## [31] "LINC00907"                 "RP11-736I24.5"            
## [33] "RP11-38B6.1"               "RP13-52K8.2"              
## [35] "TGFBI"                     "SEC14L1"                  
## [37] "PARP8"                     "IL15"                     
## [39] "APLF"                      "H2AC6"                    
## [41] "CTD-2643I7.5"             
## [1] "found 26 genes."

## [1] 34
##  [1] "ATP5F1E"       "ENOSF1"        "XAF1"          "IFI44L"       
##  [5] "ABCA8"         "FHAD1"         "PID1"          "MOBP"         
##  [9] "ODF3B"         "MX2"           "HDAC4-AS1"     "PCDH9-AS2"    
## [13] "AC073115.7"    "RP11-115J16.1" "LINC02073"     "H2BC8"        
## [17] "H2AC8"         "SLC2A3"        "PDE8A"         "RGS1"         
## [21] "DARS1"         "SRGN"          "BTG1"          "HILPDA"       
## [25] "CCNG2"         "TNFAIP8"       "ARHGAP18"      "TMEM140"      
## [29] "FRRS1"         "ALDH1A1"       "JAKMIP2"       "ADSS1"        
## [33] "ANKRD37"       "H2BU1"         "UBXN2B"        "AC093818.1"   
## [37] "DARS1-AS1"     "MIR155HG"      "SAP30-DT"      "RP11-134L10.2"
## [1] "found 29 genes."

## [1] 35
##  [1] "PDK4"     "HHAT"     "TXNDC16"  "ZNF821"   "MS4A4A"   "TENT5A"  
##  [7] "STX11"    "BRIP1"    "TNFRSF21" "NUBPL"    "B2M"      "PBX3"    
## [13] "FTH1"     "PTPRM"    "RTTN"     "GCLC"     "GCLM"     "PRKCH"   
## [19] "HACE1"    "CEP170B"  "ANKRD12"  "INTS6"    "UBE2R2"   "NCOA7"   
## [25] "SOX5"     "NHSL1"    "CPM"      "GFOD1"    "RASSF3"   "CDC42SE2"
## [31] "STARD9"   "CLASP2"   "SLMAP"    "STXBP5"   "ABCA1"    "CHD2"    
## [37] "GPRIN3"   "RALGAPA2" "ZNF277"   "DENND1B" 
## [1] "found 40 genes."

## [1] 36
##  [1] "PKD2L2"        "PCSK1N"        "CRYM"          "ANGPTL1"      
##  [5] "CALY"          "BEX3"          "RAB37"         "SPDYE2"       
##  [9] "GOLGA8B"       "SMCR5"         "RP5-1132H15.1" "LANCL1-AS1"   
## [13] "RMDN2-AS1"     "KDM4A-AS1"     "LRIG2-DT"      "MEIKIN"       
## [17] "RP11-544A12.8" "RP11-120A1.1"  "RP11-506H20.1" "RP11-624C23.1"
## [21] "RP11-867G2.8"  "RP11-571M6.7"  "RP11-317G6.1"  "RP11-66H6.3"  
## [25] "LINC00621"     "RP11-121C2.3"  "RP11-275G7.2"  "RP11-21M24.6" 
## [29] "RP11-65F13.4"  "RP11-617F9.2"  "RASGRP2"       "COL5A3"       
## [33] "IGSF9B"        "ARFGEF3"       "SNED1"         "FSTL5"        
## [37] "STXBP6"        "SRRM3"         "H1-10"         "FAM153CP"     
## [41] "LINC01322"     "RP11-322M13.1"
## [1] "found 19 genes."

## [1] 37
##  [1] "NEURL2"         "ACKR4"          "SHOC1"          "H2AC20"        
##  [5] "H2BC18"         "INSYN2B"        "ANKUB1"         "DOCK4-AS1"     
##  [9] "ARHGAP26-AS1"   "AC017101.10"    "AC037445.1"     "RP11-575L7.8"  
## [13] "CPB2-AS1"       "RP11-775D22.3"  "STARD4-AS1"     "ANK2-AS1"      
## [17] "CTD-2015H6.3"   "AC006160.5"     "RHOQ-AS1"       "LINC02196"     
## [21] "AP000487.6"     "RP11-1H15.2"    "RP11-638I2.8"   "LINC02316"     
## [25] "USP3-AS1"       "RP11-815J21.4"  "RP11-16B9.1"    "RP11-106M3.3"  
## [29] "RP11-16C1.3"    "RP11-703M24.5"  "CEACAM16-AS1"   "TCF4-AS1"      
## [33] "RP11-58G13.1"   "RP11-126O1.4"   "RP1-256G22.2"   "RP11-386I14.4" 
## [37] "RP11-793H13.14" "RP11-622I12.1"  "RP11-314L11.1"  "RP11-1H15.4"   
## [41] "RP11-6G22.1"    "RP11-555K12.4" 
## [1] "found 7 genes."

## [1] 38
##  [1] "IGF1"          "RPL3"          "RPL18A"        "RPL19"        
##  [5] "RPL34"         "RPL24"         "IFIT3"         "IFIT2"        
##  [9] "FGF13"         "RPLP1"         "RPS24"         "PRDM5"        
## [13] "RPS2"          "RPS11"         "RPL11"         "RPS27A"       
## [17] "RPL32"         "FAU"           "ATG10"         "RPL26"        
## [21] "ELAVL4"        "NFIA"          "RPL38"         "RPLP2"        
## [25] "TSPYL2"        "IFIT1"         "RPS23"         "SPATS2L"      
## [29] "CPNE4"         "RPL12"         "RPL23A"        "AIF1"         
## [33] "RP11-511B23.2" "SPOCK2"        "SLC1A2"        "ZMAT4"        
## [37] "ADARB1"        "SKIV2L"       
## [1] "found 36 genes."

## [1] 39
##  [1] "ABCB4"         "NAV3"          "TTC7A"         "FAM149A"      
##  [5] "PLCL1"         "GARNL3"        "GIPC2"         "GPAT3"        
##  [9] "GASK1A"        "ITGA9"         "DPYS"          "TENM4"        
## [13] "TMEM163"       "SETBP1"        "LIPC"          "NAV2"         
## [17] "CX3CR1"        "ZMAT3"         "TCERG1L"       "RP1-30E17.2"  
## [21] "AC105760.2"    "MIR646HG"      "HDAC2-AS2"     "LINC00884"    
## [25] "RP11-120D5.1"  "PTCHD4"        "LINC00968"     "LINC02762"    
## [29] "ZFPM2-AS1"     "LINC01301"     "RP11-10H3.1"   "RP11-541P9.3" 
## [33] "RP11-370I10.6" "MEI4"          "CTTNBP2"       "CUX2"         
## [37] "DPYSL3"        "WDR45B"        "NCMAP"         "EME2"         
## [41] "LINC01435"     "RP11-452F19.4"
## [1] "found 27 genes."

## [1] 40
##  [1] "ATP8B1"        "OMD"           "IRAG1-AS1"     "SCOC-AS1"     
##  [5] "MTCP1"         "RP11-321C24.1" "AC023590.1"    "ZNF451-AS1"   
##  [9] "RP11-165F24.3" "ALG13-AS1"     "RP1-225E12.2"  "AC083884.8"   
## [13] "RP1-117O3.2"   "KCNMA1-AS1"    "BCL2L1-AS1"    "RP11-544A12.4"
## [17] "LINC01877"     "RP5-1101C3.1"  "ZBTB20-AS5"    "LINC00960"    
## [21] "FAM198B-AS1"   "RP11-39E3.3"   "CTD-3239E11.2" "RP11-434H14.1"
## [25] "RP1-71H24.1"   "RP11-713N11.4" "CTD-2647E9.3"  "PRKCA-AS1"    
## [29] "RP11-737O24.2" "RP11-53B2.3"   "CTD-3149D2.4"  "RP4-769N13.7" 
## [33] "RP11-354K4.2"  "RP11-458A7.1"  "RP11-261A24.1" "RP1-18C9.3"   
## [37] "RP11-13J12.3"  "RP11-685G9.5"  "RP11-341N18.1" "RP11-399K19.1"
## [41] "CTD-2021K4.2"  "CCDC71L"      
## [1] "found 4 genes."

Session information

gc()

##           used  (Mb) gc trigger  (Mb) limit (Mb) max used  (Mb)
## Ncells 4174736 223.0   10243768 547.1         NA 10243768 547.1
## Vcells 8946275  68.3   29538339 225.4      65536 29538339 225.4

sessionInfo()

## R version 4.2.3 (2023-03-15)
## Platform: aarch64-apple-darwin20 (64-bit)
## Running under: macOS Ventura 13.4.1
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] stringr_1.5.0     limma_3.54.2      tidyr_1.3.0       ggpubr_0.6.0     
## [5] ggplot2_3.4.2     data.table_1.14.8
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_1.0.10            png_0.1-8              Biostrings_2.66.0     
##  [4] digest_0.6.31          utf8_1.2.3             R6_2.5.1              
##  [7] GenomeInfoDb_1.34.9    backports_1.4.1        stats4_4.2.3          
## [10] RSQLite_2.3.1          evaluate_0.20          httr_1.4.6            
## [13] pillar_1.9.0           zlibbioc_1.44.0        rlang_1.1.0           
## [16] rstudioapi_0.14        car_3.1-2              jquerylib_0.1.4       
## [19] blob_1.2.4             R.oo_1.25.0            R.utils_2.12.2        
## [22] S4Vectors_0.36.2       rmarkdown_2.21         labeling_0.4.2        
## [25] RCurl_1.98-1.12        bit_4.0.5              munsell_0.5.0         
## [28] broom_1.0.4            compiler_4.2.3         xfun_0.39             
## [31] pkgconfig_2.0.3        BiocGenerics_0.44.0    htmltools_0.5.5       
## [34] tidyselect_1.2.0       KEGGREST_1.38.0        GenomeInfoDbData_1.2.9
## [37] tibble_3.2.1           IRanges_2.32.0         fansi_1.0.4           
## [40] crayon_1.5.2           dplyr_1.1.2            withr_2.5.0           
## [43] R.methodsS3_1.8.2      bitops_1.0-7           grid_4.2.3            
## [46] jsonlite_1.8.4         gtable_0.3.3           lifecycle_1.0.3       
## [49] DBI_1.1.3              magrittr_2.0.3         scales_1.2.1          
## [52] cli_3.6.1              stringi_1.7.12         cachem_1.0.7          
## [55] carData_3.0-5          farver_2.1.1           XVector_0.38.0        
## [58] ggsignif_0.6.4         bslib_0.4.2            generics_0.1.3        
## [61] vctrs_0.6.2            RColorBrewer_1.1-3     org.Hs.eg.db_3.16.0   
## [64] tools_4.2.3            bit64_4.0.5            Biobase_2.58.0        
## [67] glue_1.6.2             purrr_1.0.1            abind_1.4-5           
## [70] fastmap_1.1.1          yaml_2.3.7             AnnotationDbi_1.60.2  
## [73] colorspace_2.1-0       rstatix_0.7.2          memoise_2.0.1         
## [76] knitr_1.44             sass_0.4.5